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Yorodumi- PDB-1n9o: Crystal structure of the Phot-LOV1 domain from Chlamydomonas rein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n9o | ||||||
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Title | Crystal structure of the Phot-LOV1 domain from Chlamydomonas reinhardtii in illuminated state. Composite data set. | ||||||
Components | putative blue light receptor | ||||||
Keywords | ELECTRON TRANSPORT / phototropin / flavin | ||||||
Function / homology | Function and homology information blue light signaling pathway / blue light photoreceptor activity / protein autophosphorylation / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Fedorov, R. / Schlichting, I. / Hartmann, E. / Domratcheva, T. / Fuhrmann, M. / Hegemann, P. | ||||||
Citation | Journal: Biophys.J. / Year: 2003 Title: Crystal structures and molecular mechanism of a light-induced signaling switch: The Phot-LOV1 domain from Chlamydomonas reinhardtii. Authors: Fedorov, R. / Schlichting, I. / Hartmann, E. / Domratcheva, T. / Fuhrmann, M. / Hegemann, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n9o.cif.gz | 36.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n9o.ent.gz | 23.8 KB | Display | PDB format |
PDBx/mmJSON format | 1n9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n9o_validation.pdf.gz | 771.3 KB | Display | wwPDB validaton report |
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Full document | 1n9o_full_validation.pdf.gz | 775.5 KB | Display | |
Data in XML | 1n9o_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1n9o_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/1n9o ftp://data.pdbj.org/pub/pdb/validation_reports/n9/1n9o | HTTPS FTP |
-Related structure data
Related structure data | 1n9lC 1n9nC 1g28S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11989.646 Da / Num. of mol.: 1 / Fragment: residues 17-125 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Plasmid: pET16 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8LPE0, UniProt: Q8LPD9*PLUS |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-FMN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 68.13 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: HEPES, ammonium sulfate, PEG8000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.8→15 Å / Num. all: 5264 / Num. obs: 5009 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 36.8 Å2 / Rsym value: 0.129 / Net I/σ(I): 7.5 | ||||||||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.322 / % possible all: 82.5 | ||||||||||||||||||
Reflection | *PLUS Num. all: 16983 / Rmerge(I) obs: 0.129 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 82.5 % / Rmerge(I) obs: 0.322 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G28 Resolution: 2.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rwork: 0.25 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |